Proliferation_ModID
2023-05-29
Looking for modules in Proliferating CD4
Much of the opioid literature suggests that proliferating CD4 are responsible for a large part of the opioid dependent CD4 impact. Objective here is to try and identify those modules. See module RMD for more of the intuition/logic as to choices made.
Possible comparisons
There are many iterations we could select for this analysis, from most ideal to least ideal: * Participant + Treatment + Timepoint * Treatment + Timepoint * Participant + Treatment * Treatment
Which can further be expanded to which CD4 populations are included. A more robust CD4 module ID will occur at a later point. First we just subset proliferating cells, then we get the parts of those that are in each subset.
results<-subset(results, idents = "Proliferating")## Loading required package: Signactable(results$Treatment)##
## Bup.Nalo Methadone Naltrexone
## 330 56 138table(results$Timepoint)##
## 0 3
## 197 327table(paste(results$Treatment, results$Timepoint))##
## Bup.Nalo 0 Bup.Nalo 3 Methadone 0 Methadone 3 Naltrexone 0 Naltrexone 3
## 101 229 13 43 83 55table(paste(results$Treatment, results$Participant))##
## Bup.Nalo 5014 Bup.Nalo 5017 Bup.Nalo 5018 Bup.Nalo 5023 Methadone 5003
## 42 145 133 10 10
## Methadone 5009 Methadone 5016 Methadone 5020 Naltrexone 5021 Naltrexone 5026
## 22 11 13 7 59
## Naltrexone 5035 Naltrexone 5037
## 17 55table(paste(results$Treatment, results$Timepoint, results$Participant))##
## Bup.Nalo 0 5014 Bup.Nalo 0 5017 Bup.Nalo 0 5018 Bup.Nalo 0 5023
## 7 37 54 3
## Bup.Nalo 3 5014 Bup.Nalo 3 5017 Bup.Nalo 3 5018 Bup.Nalo 3 5023
## 35 108 79 7
## Methadone 0 5003 Methadone 0 5009 Methadone 0 5016 Methadone 0 5020
## 4 1 4 4
## Methadone 3 5003 Methadone 3 5009 Methadone 3 5016 Methadone 3 5020
## 6 21 7 9
## Naltrexone 0 5021 Naltrexone 0 5026 Naltrexone 0 5035 Naltrexone 0 5037
## 3 33 8 39
## Naltrexone 3 5021 Naltrexone 3 5026 Naltrexone 3 5035 Naltrexone 3 5037
## 4 26 9 16We need “enough” cells to have a hope of identifying modules. “Enough” is a hard call, but in my experience, around 50 cells are needed to call a module. Clearly the most desirable (treatment, timepoint, and participant specific) is not sufficient to call modules. Treatment + pariticipant also has too few cells in the methadone and Naltrexone groups to ID modules. Treatment timepoint is borderline for all except methadone time 0, but seems close enough to try at least. Timepoint and treatment alone both have sufficient cells, and we can try to call modules with them.
results$T_TP<-paste(results$Treatment, results$Timepoint, sep="_")
results.split<-SplitObject(results, "T_TP")
#npcs and softpowers, selecting npc based on last nonplataue pc on elbow plot, selecting softpower as first above 0.8
#nothing for methadone, PCA doesnt have enough observations, go modules for the other two
conds<-cbind(c(7,6, 7, 9,1,1),c(5,9, 8, 14,1,1 ))
mods1<-WrapGroupModID(results.split, "NA", conds)## [1] "Bup.Nalo_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.3816## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49885## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.207e-15## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## PC_ 1
## Positive: RRM2, DIAPH3, POLQ, NCAPG, HIST1H1B, SMC2, TOP2A, NCAPG2, MKI67, NUSAP1
## SHCBP1, CENPP, FBXO5, FANCI, ASPM, ATAD5, KIF15, KNL1, TUBB, TUBA1B
## Negative: LTB, XIST, ANK3, TTN, JUNB, FMN1, AP000787.1, MPP7, LINC01934, ZNF331
## AC105402.3, MAML2, SESN3, DPYD-AS1, UST, TOX, FAAH2, JUN, FAM13A, DUSP2
## PC_ 2
## Positive: RPTOR, SLFN12L, MGAT5, UTY, MTAP, CASK, POLQ, KIF18B, ATAD5, HIVEP1
## KNTC1, CIT, WWOX, ZNF236, SNX29, BTBD11, FANCD2, PITPNC1, POLE, RAP1GAP2
## Negative: RPS2, RPL41, RPL28, RPS15, RPL27A, RPS18, RPL18A, PFN1, RPLP1, RPL13A
## RPS16, RPS12, TMSB4X, RPL18, RPS19, GAPDH, TMSB10, RPS23, RPS28, RPS27
## PC_ 3
## Positive: PLK1, KIF14, HMMR, PIF1, CDCA2, SGO2, CCNB1, INCENP, KIF20A, AURKA
## UBE2C, KIF2C, KIF4A, CCNB2, KPNA2, SPDL1, TOP2A, ASPM, KIF18B, KIF23
## Negative: MIR4422HG, PECAM1, DTHD1, MCTP2, GZMK, LYST, PTPN3, NCOA1, MYB, PON2
## HAVCR2, SESTD1, CD38, SAMD3, LRMP, AL031599.1, PACSIN1, POU2AF1, DNAJC1, TRPS1
## PC_ 4
## Positive: MIR4422HG, PECAM1, PTPN3, GZMK, LYST, MCTP2, NKG7, DTHD1, KPNA2, AGAP1
## AL031599.1, FXYD2, LRMP, CBLB, UBE2E2, SESTD1, HAVCR2, CENPF, PTPRE, KIF20A
## Negative: AKT3, FKBP5, MSH6, SSBP2, SCFD2, MPP6, LTB, FANCA, GPHN, CDC6
## PUS7, ORC6, TANC2, SNED1, DISC1, RBBP8, DTL, CDC45, FAM111B, CCNE2
## PC_ 5
## Positive: KCNQ5, AGAP1, E2F7, CCNE2, HIST1H1D, AFF3, XIST, PECAM1, C1orf21, SKA3
## KLRK1, HIST1H3D, GZMK, RFC3, HIST1H2BM, CSRP3-AS1, CDCA5, CD8B, CREB5, NEIL3
## Negative: PLCL1, MGAT5, RORA, NEAT1, AL136456.1, UTY, CDHR3, ABLIM1, LINC02384, IQGAP2
## CLIC5, CD59, IL6R, LGMN, IL2RA, SGO1-AS1, LINC00278, MAST4, MRPL33, MTERF1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.0298 1.71 0.5850 148.000 1.46e+02 166.00
## 2 2 0.4170 -2.69 0.6070 79.800 7.74e+01 103.00
## 3 3 0.6290 -2.44 0.7540 44.200 4.18e+01 67.20
## 4 4 0.7880 -2.26 0.8790 25.300 2.27e+01 46.20
## 5 5 0.8600 -2.04 0.8770 15.000 1.25e+01 33.30
## 6 6 0.8170 -1.95 0.7980 9.190 7.01e+00 24.80
## 7 7 0.8540 -1.76 0.8290 5.870 3.98e+00 19.10
## 8 8 0.7580 -1.73 0.7100 3.890 2.27e+00 15.00
## 9 9 0.7750 -1.62 0.7440 2.670 1.33e+00 12.00
## 10 10 0.2290 -3.22 0.1260 1.890 7.84e-01 9.79
## 11 12 0.8820 -1.34 0.9150 1.030 2.86e-01 6.69
## 12 14 0.8360 -1.24 0.8620 0.606 1.18e-01 4.72
## 13 16 0.2010 -2.15 0.0357 0.378 4.94e-02 3.42
## 14 18 0.2100 -2.06 0.0432 0.245 2.15e-02 2.51
## 15 20 0.8700 -1.22 0.9110 0.163 9.63e-03 1.88
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8 9 10
## 9 72 47 36 24 24 20 13 13 13 12
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 11 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.## $blue
## [1] "RRM2" "DIAPH3" "POLQ" "NCAPG" "HIST1H1B"
## [6] "SMC2" "TOP2A" "NCAPG2" "MKI67" "NUSAP1"
## [11] "SHCBP1" "CENPP" "FBXO5" "FANCI" "ASPM"
## [16] "ATAD5" "KIF15" "KNL1" "TUBB" "TUBA1B"
## [21] "TMPO" "DTL" "SPC25" "STMN1" "CIT"
## [26] "AL136456.1" "RPTOR" "SLFN12L" "MGAT5" "UTY"
## [31] "MTAP" "KIF18B" "HIVEP1" "KNTC1" "WWOX"
## [36] "ZNF236" "SNX29" "BTBD11" "FANCD2" "POLE"
## [41] "RAP1GAP2" "RBL1" "RORA" "WDHD1" "PCNT"
## [46] "IQGAP2" "PLK1" "KIF14" "HMMR" "PIF1"
## [51] "CDCA2" "SGO2" "CCNB1" "INCENP" "KIF20A"
## [56] "AURKA" "UBE2C" "KIF2C" "KIF4A" "CCNB2"
## [61] "KPNA2" "SPDL1" "KIF23" "CCNF" "ESPL1"
## [66] "CDCA8" "CKAP2L" "DEPDC1B" "MYB" "SAMD3"
## [71] "CENPF" "MSH6" "SSBP2" "SCFD2" "MPP6"
## [76] "FANCA" "GPHN" "CDC6" "PUS7" "ORC6"
## [81] "TANC2" "RBBP8" "CDC45" "FAM111B" "CCNE2"
## [86] "USP37" "WDR76" "HELLS" "E2F7" "HIST1H1D"
## [91] "SKA3" "HIST1H3D" "RFC3" "HIST1H2BM" "CDCA5"
## [96] "NEIL3" "UHRF1" "MCM10" "RAD51AP1" "PLCL1"
## [101] "NEAT1" "CDHR3" "ABLIM1" "LINC02384" "CLIC5"
## [106] "CD59" "IL6R" "LGMN" "IL2RA" "SGO1-AS1"
## [111] "LINC00278" "MAST4" "MTERF1" "ADD3-AS1" "TEX9"
## [116] "GPR15" "RFX3-AS1" "RFX3" "ZRANB3" "PPP3CA"
## [121] "HSP90AA1" "AGPAT4" "KHDC1" "SYTL2" "TNFRSF1B"
## [126] "CLSPN" "HMGB1" "BIRC5" "DNMT1" "AUTS2"
## [131] "TPM4" "TXK" "PRKCA" "SELL" "HIST1H2BK"
## [136] "BACH2" "XYLB" "MCM5" "PXMP2" "IGF1R"
## [141] "PLAGL1" "DMC1" "F5"
##
## $purple
## [1] "LTB" "ANK3" "JUNB" "FMN1" "AP000787.1"
## [6] "MPP7" "ZNF331" "SESN3" "DPYD-AS1" "SPON1"
## [11] "SNED1" "FHIT"
##
## $black
## [1] "XIST" "TTN" "TOX" "FAM13A" "CCDC141"
## [6] "CDK14" "AC093865.1" "CPM" "RBMS3" "IKZF2"
## [11] "MAGI1" "MIR181A1HG" "ST8SIA1"
##
## $magenta
## [1] "LINC01934" "UST" "MCF2L2" "MRPL33" "TRERF1"
## [6] "MSC-AS1" "AC104073.4" "IQCJ-SCHIP1" "CTSW" "RBPJ"
## [11] "BFSP1" "LINC02694" "HOPX"
##
## $brown
## [1] "DUSP2" "RPS2" "RPL41" "RPL28" "RPS15" "RPL27A" "RPS18"
## [8] "RPL18A" "PFN1" "RPLP1" "RPL13A" "RPS16" "RPS12" "TMSB4X"
## [15] "RPL18" "RPS19" "GAPDH" "TMSB10" "RPS23" "RPS28" "RPS27"
## [22] "RPLP2" "RPL37" "RPS4X" "RPL37A" "RPL11" "C1orf21" "CALM1"
## [29] "IL18RAP" "ATP5F1E" "ANXA1" "ENO1" "CORO1A" "SMIM20" "MAP3K8"
## [36] "RPS6"
##
## $red
## [1] "AFF3" "CASK" "PITPNC1" "MIR4422HG" "PECAM1"
## [6] "DTHD1" "MCTP2" "GZMK" "LYST" "PTPN3"
## [11] "NCOA1" "PON2" "HAVCR2" "SESTD1" "CD38"
## [16] "LRMP" "AL031599.1" "PACSIN1" "POU2AF1" "DNAJC1"
## [21] "TRPS1" "GTDC1" "IL19" "AGAP1" "LGALS3"
## [26] "ZSWIM6" "FXYD2" "CBLB" "UBE2E2" "PTPRE"
## [31] "TNIP3" "AL603840.1" "KCNQ5" "KLRK1" "CSRP3-AS1"
## [36] "CREB5" "PAM" "LINC02614" "PRELID2" "SRGAP2B"
## [41] "TRAV19" "MTRNR2L8" "ABCB1" "NEDD4L"
##
## $pink
## [1] "NKG7" "CD8B" "CCL5" "TGFBR3" "ZEB2" "HLA-DPA1"
## [7] "HLA-DRB1" "HLA-DRB5" "GZMA" "GAB3" "MVB12B" "CD74"
## [13] "NFIL3"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "9588/10000 permutations failed the Mann-Whitney test."
## [1] "9917/10000 permutations failed the Mann-Whitney test."
## [1] "9957/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "8848/10000 permutations failed the Mann-Whitney test."
## [1] "9442/10000 permutations failed the Mann-Whitney test."
## $blue
## [1] "RRM2" "DIAPH3" "POLQ" "NCAPG" "HIST1H1B"
## [6] "SMC2" "TOP2A" "NCAPG2" "MKI67" "NUSAP1"
## [11] "SHCBP1" "CENPP" "FBXO5" "FANCI" "ASPM"
## [16] "ATAD5" "KIF15" "KNL1" "TUBB" "TUBA1B"
## [21] "TMPO" "DTL" "SPC25" "STMN1" "CIT"
## [26] "AL136456.1" "RPTOR" "SLFN12L" "MGAT5" "UTY"
## [31] "MTAP" "KIF18B" "HIVEP1" "KNTC1" "WWOX"
## [36] "ZNF236" "SNX29" "BTBD11" "FANCD2" "POLE"
## [41] "RAP1GAP2" "RBL1" "RORA" "WDHD1" "PCNT"
## [46] "IQGAP2" "PLK1" "KIF14" "HMMR" "PIF1"
## [51] "CDCA2" "SGO2" "CCNB1" "INCENP" "KIF20A"
## [56] "AURKA" "UBE2C" "KIF2C" "KIF4A" "CCNB2"
## [61] "KPNA2" "SPDL1" "KIF23" "CCNF" "ESPL1"
## [66] "CDCA8" "CKAP2L" "DEPDC1B" "MYB" "SAMD3"
## [71] "CENPF" "MSH6" "SSBP2" "SCFD2" "MPP6"
## [76] "FANCA" "GPHN" "CDC6" "PUS7" "ORC6"
## [81] "TANC2" "RBBP8" "CDC45" "FAM111B" "CCNE2"
## [86] "USP37" "WDR76" "HELLS" "E2F7" "HIST1H1D"
## [91] "SKA3" "HIST1H3D" "RFC3" "HIST1H2BM" "CDCA5"
## [96] "NEIL3" "UHRF1" "MCM10" "RAD51AP1" "PLCL1"
## [101] "NEAT1" "CDHR3" "ABLIM1" "LINC02384" "CLIC5"
## [106] "CD59" "IL6R" "LGMN" "IL2RA" "SGO1-AS1"
## [111] "LINC00278" "MAST4" "MTERF1" "ADD3-AS1" "TEX9"
## [116] "GPR15" "RFX3-AS1" "RFX3" "ZRANB3" "PPP3CA"
## [121] "HSP90AA1" "AGPAT4" "KHDC1" "SYTL2" "TNFRSF1B"
## [126] "CLSPN" "HMGB1" "BIRC5" "DNMT1" "AUTS2"
## [131] "TPM4" "TXK" "PRKCA" "SELL" "HIST1H2BK"
## [136] "BACH2" "XYLB" "MCM5" "PXMP2" "IGF1R"
## [141] "PLAGL1" "DMC1" "F5"
##
## $brown
## [1] "DUSP2" "RPS2" "RPL41" "RPL28" "RPS15" "RPL27A" "RPS18"
## [8] "RPL18A" "PFN1" "RPLP1" "RPL13A" "RPS16" "RPS12" "TMSB4X"
## [15] "RPL18" "RPS19" "GAPDH" "TMSB10" "RPS23" "RPS28" "RPS27"
## [22] "RPLP2" "RPL37" "RPS4X" "RPL37A" "RPL11" "C1orf21" "CALM1"
## [29] "IL18RAP" "ATP5F1E" "ANXA1" "ENO1" "CORO1A" "SMIM20" "MAP3K8"
## [36] "RPS6"
##
## [1] "Bup.Nalo_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.0243## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49706## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 7.9876e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: PCAT1, FOXP1, ABLIM1, ANK3, C22orf34, INPP5A, SESN3, FAAH2, SCML4, TSHZ2
## GMDS-DT, AL136456.1, EXOC6B, FHIT, CCDC18-AS1, PRKCQ, IMMP2L, ATP10A, EHBP1, AC233976.1
## Negative: TUBA1B, SLC25A5, TYMS, TUBB, GAPDH, STMN1, PFN1, TPI1, ACTB, PSMA7
## HIST1H4C, TK1, RRM2, LDHA, HMGB2, TUBB4B, BIRC5, CLSPN, HNRNPAB, RPSA
## PC_ 2
## Positive: RPL28, B2M, RPL27A, RPL11, RPL10, RPS19, RPS28, RPS12, RPL30, RPL41
## RPS23, RPS16, RPS29, RPL13, RPS15A, RPL37A, RPLP1, RPS27, RPS15, RPS18
## Negative: KIF18B, SPC25, MELK, CIT, ANLN, POLQ, RAD54L, BRCA2, MKI67, NCAPG2
## PLK4, DIAPH3, KIF11, NUSAP1, MASTL, KIF15, CENPE, KNTC1, CCNF, NCAPG
## PC_ 3
## Positive: STAM, KIF14, MAP3K1, IL2RA, CDCA8, KIF4A, KLF2, LTB, CKAP2L, MAF
## APOLD1, ESPL1, FOXP1, SESN3, HIST2H2AB, ASPM, RPS3A, CKS1B, ARHGAP11A, TMSB10
## Negative: NKG7, KCNQ5, MTHFD1, KLRK1, ZEB2, ARHGAP26, MTHFD1L, SH3RF2, TMEM241, CDC45
## CADM1, PRKD3, UNG, FEN1, SLBP, FAM50B, SFMBT2, PECAM1, C1orf21, TIMM13
## PC_ 4
## Positive: FLT1, LINC00665, NOP16, SUPT3H, GNB4, RAB33B, TRBV5-1, TRPS1, FAM104B, MIR4422HG
## SUPT4H1, PIP4K2A, CLDND1, PDZRN3, IMPDH2, ZSCAN5A, RAP1GDS1, ZNF211, TMEM131L, LINC00886
## Negative: SETBP1, NUP155, FANCA, CCL5, CLSPN, FANCB, ATAD5, CENPP, EXO1, E2F7
## IL12RB2, RHBDF2, SLC12A8, SLC12A2, HLA-DQA1, SFMBT2, BRIP1, RPL10A, BCL7A, LYAR
## PC_ 5
## Positive: TSHZ2, RPS6KA2, CIB1, ABLIM1, AL136456.1, AC009522.1, SDCBP2-AS1, FUT7, RORA, DIPK2A
## TRBV5-1, TCTN1, APH1A, MAP7, PDIA4, EIF2S1, ARNTL2, SYCP2, MGAT5, NME1
## Negative: SESTD1, LYST, PECAM1, ALCAM, DTHD1, PTPN3, AL031599.1, RAP1GDS1, GZMK, IKZF2
## GALNT1, UBE2E2, CBLB, MCTP1, SFMBT2, STK33, ADGRA3, LINC02631, RNF14, AC093865.1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.1740 3.000 0.792 147.000 148.0000 165.00
## 2 2 0.0256 0.487 0.748 80.800 80.6000 103.00
## 3 3 0.0485 -0.398 0.618 45.800 44.7000 66.50
## 4 4 0.2640 -0.732 0.550 27.000 25.4000 44.50
## 5 5 0.5050 -0.968 0.710 16.500 14.8000 31.70
## 6 6 0.6420 -1.090 0.738 10.500 8.8700 23.40
## 7 7 0.7070 -1.180 0.728 6.890 5.4600 17.80
## 8 8 0.7750 -1.260 0.789 4.710 3.4400 14.00
## 9 9 0.8010 -1.260 0.818 3.330 2.1600 11.20
## 10 10 0.8120 -1.230 0.813 2.420 1.4300 9.17
## 11 12 0.8640 -1.170 0.883 1.380 0.6830 6.34
## 12 14 0.7620 -1.200 0.764 0.854 0.3420 4.54
## 13 16 0.7800 -1.140 0.776 0.557 0.1740 3.32
## 14 18 0.8570 -1.080 0.882 0.379 0.0919 2.47
## 15 20 0.8420 -1.060 0.859 0.267 0.0499 1.86
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8 9
## 144 24 23 19 14 13 10 10 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 10 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $black
## [1] "TUBA1B" "SLC25A5" "TYMS" "TUBB" "STMN1" "TPI1"
## [7] "PSMA7" "HIST1H4C" "TK1" "LDHA" "HMGB2" "TUBB4B"
## [13] "BIRC5" "CLSPN" "HNRNPAB" "MT2A" "ENO1" "KIF18B"
## [19] "SPC25" "MELK" "CIT" "ANLN" "POLQ" "RAD54L"
## [25] "BRCA2" "NCAPG2" "PLK4" "NUSAP1" "MASTL" "KNTC1"
## [31] "BRIP1" "ASPM" "BUB1B" "KIF14" "CDCA8" "KIF4A"
## [37] "CKAP2L" "ESPL1" "HIST2H2AB" "CKS1B" "ARHGAP11A" "NCAPH"
## [43] "HJURP" "KCNQ5" "CDC45" "SLBP" "TIMM13" "HSPD1"
## [49] "DTL" "MCM4" "TRBV5-1" "FANCA" "FANCB" "ATAD5"
## [55] "CENPP" "EXO1" "E2F7" "SLC12A8" "BRCA1" "MSH6"
## [61] "FUT7" "CX3CR1" "UHRF1" "WARS2" "LRRC20" "ACTL6A"
## [67] "PIGM"
##
## $green
## [1] "GAPDH" "PFN1" "ACTB" "RPSA" "HNRNPA1"
## [6] "ACTG1" "CFL1" "RPL28" "B2M" "RPL27A"
## [11] "RPL11" "RPL10" "RPS19" "RPS28" "RPS12"
## [16] "RPL30" "RPL41" "RPS23" "RPS16" "RPS29"
## [21] "RPL13" "RPS15A" "RPL37A" "RPLP1" "RPS27"
## [26] "RPS15" "RPS18" "RPL12" "RPL18A" "RPLP2"
## [31] "RPS20" "RPL18" "LTB" "RPS3A" "TMSB10"
## [36] "RPL10A" "AC008937.2"
##
## $red
## [1] "PECAM1" "MIR4422HG" "RAP1GDS1" "SESTD1" "LYST"
## [6] "PTPN3" "AL031599.1" "UBE2E2" "STK33" "DGKH"
##
## $brown
## [1] "RHBDF2" "BCL7A" "AC009522.1" "APH1A" "PDIA4"
## [6] "NME1" "CDK2AP2" "COBLL1" "PIK3AP1" "ATP1B1"
## [11] "MZB1" "METTL22" "SYK" "MRPL51" "TRIO"
## [16] "FGD4" "NHP2" "NOLC1" "SLC8A1"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $black
## [1] "TUBA1B" "SLC25A5" "TYMS" "TUBB" "STMN1" "TPI1"
## [7] "PSMA7" "HIST1H4C" "TK1" "LDHA" "HMGB2" "TUBB4B"
## [13] "BIRC5" "CLSPN" "HNRNPAB" "MT2A" "ENO1" "KIF18B"
## [19] "SPC25" "MELK" "CIT" "ANLN" "POLQ" "RAD54L"
## [25] "BRCA2" "NCAPG2" "PLK4" "NUSAP1" "MASTL" "KNTC1"
## [31] "BRIP1" "ASPM" "BUB1B" "KIF14" "CDCA8" "KIF4A"
## [37] "CKAP2L" "ESPL1" "HIST2H2AB" "CKS1B" "ARHGAP11A" "NCAPH"
## [43] "HJURP" "KCNQ5" "CDC45" "SLBP" "TIMM13" "HSPD1"
## [49] "DTL" "MCM4" "TRBV5-1" "FANCA" "FANCB" "ATAD5"
## [55] "CENPP" "EXO1" "E2F7" "SLC12A8" "BRCA1" "MSH6"
## [61] "FUT7" "CX3CR1" "UHRF1" "WARS2" "LRRC20" "ACTL6A"
## [67] "PIGM"
##
## $green
## [1] "GAPDH" "PFN1" "ACTB" "RPSA" "HNRNPA1"
## [6] "ACTG1" "CFL1" "RPL28" "B2M" "RPL27A"
## [11] "RPL11" "RPL10" "RPS19" "RPS28" "RPS12"
## [16] "RPL30" "RPL41" "RPS23" "RPS16" "RPS29"
## [21] "RPL13" "RPS15A" "RPL37A" "RPLP1" "RPS27"
## [26] "RPS15" "RPS18" "RPL12" "RPL18A" "RPLP2"
## [31] "RPS20" "RPL18" "LTB" "RPS3A" "TMSB10"
## [36] "RPL10A" "AC008937.2"
##
## $red
## [1] "PECAM1" "MIR4422HG" "RAP1GDS1" "SESTD1" "LYST"
## [6] "PTPN3" "AL031599.1" "UBE2E2" "STK33" "DGKH"
##
## $brown
## [1] "RHBDF2" "BCL7A" "AC009522.1" "APH1A" "PDIA4"
## [6] "NME1" "CDK2AP2" "COBLL1" "PIK3AP1" "ATP1B1"
## [11] "MZB1" "METTL22" "SYK" "MRPL51" "TRIO"
## [16] "FGD4" "NHP2" "NOLC1" "SLC8A1"
##
## [1] "Naltrexone_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.9386## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.3206## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.2557e-30## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.
## PC_ 1
## Positive: RRM2, POLQ, NCAPG2, KIF11, ECT2, DIAPH3, ASPM, KIF14, NCAPG, CDCA2
## DLGAP5, HIST1H3B, HIST1H1B, SPC25, TPX2, TOP2A, BRCA2, KIF15, CCDC150, NUF2
## Negative: PITPNC1, SESN3, AFF3, ZNF331, SLC2A3, MPP7, TSHZ2, AC137810.1, KIAA0825, MTRNR2L8
## TMEM164, PDE7A, AC104123.1, KCNQ1OT1, RAP2C-AS1, ATP11C, JUN, SNHG14, GRIK1, CD5
## PC_ 2
## Positive: MTRNR2L8, CIT, HJURP, KIF11, TPX2, NCAPH, HIST1H4H, RRM2, KIF4A, HIST1H2AG
## DLGAP5, INCENP, HMGB2, GTSE1, POLQ, ASPM, PTMA, KIF15, HIST1H1B, KNL1
## Negative: ACO1, RFX3, CELF2, MUC20, KLF12, EXOC4, ZBTB20, N4BP1, TSHZ2, MBNL1
## AC106791.1, AL606491.1, TMEM63A, ANKMY1, ATXN1, MAP3K4, MGLL, LONRF1, RORA, AL050309.1
## PC_ 3
## Positive: RPS23, RPS2, RPL41, RPS12, IL32, RPS16, TMSB10, FAU, RPS15, GAPDH
## ACTG1, B2M, RPL15, CRIP1, RPL21, RPS13, AC079793.1, PFN1, S100A4, MZT2B
## Negative: WWOX, E2F2, DDX11, ZNF367, RASA3, CD99L2, SPC25, KIFC1, LINC00265, CDK19
## AL136456.1, RAD51, POGLUT3, ATAD5, FOXP1, TACC3, CRACR2A, RNF144B, DEPDC1B, OTULINL
## PC_ 4
## Positive: CCDC58, LINC00299, PROK2, DIP2C, KHDC1, ATPAF1, TPRG1L, TXNDC16, FILNC1, AC008549.2
## FARSB, FAM111B, RAI1, MCM4, ZNF71, PAK1, SDHAF3, CPEB3, PLD1, AC074032.1
## Negative: AL606491.1, AC079142.1, LIMK1, ZBTB24, HSF5, FIRRE, UBA6-AS1, PACS1, TSPAN17, CDRT4
## HCG17, TXK, DPH5, MRPS6, SLX4IP, ARHGAP11B, PRH1, AC092683.1, ENOX2, CENPV
## PC_ 5
## Positive: SLC39A8, AC017071.1, G2E3-AS1, FILNC1, ZNF71, TNFAIP3, ELOVL4, PARL, EPHB1, LIPE-AS1
## ETV6, TIGAR, CRLS1, COPA, MYLIP, AP002807.1, ZNF331, PROSER3, CNOT6L, SMYD3
## Negative: COLQ, PPM1L, CENPP, HSF5, NKG7, AC017028.1, FSD1L, CCDC171, TBRG4, MRPL20-AS1
## GUSB, CDT1, NEXN, RUNX2, INSL6, PDCD11, ERLIN1, NUDCD1, ADCY3, UBE2A
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.37300 12.0000 0.819 165.000 165.0000 179.00
## 2 2 0.17800 2.7500 0.789 89.800 89.6000 107.00
## 3 3 0.00046 -0.0789 0.670 50.300 49.7000 69.10
## 4 4 0.17200 -1.1500 0.737 29.200 28.3000 47.80
## 5 5 0.42300 -1.5800 0.728 17.500 16.4000 35.30
## 6 6 0.58700 -1.5900 0.783 11.000 9.8000 27.40
## 7 7 0.74000 -1.6400 0.802 7.150 6.0500 22.30
## 8 8 0.79400 -1.9000 0.806 4.860 3.8400 18.60
## 9 9 0.86600 -1.8400 0.854 3.440 2.5400 15.90
## 10 10 0.90000 -1.7500 0.888 2.530 1.7000 13.90
## 11 12 0.91900 -1.6100 0.901 1.500 0.7830 10.90
## 12 14 0.96100 -1.4700 0.953 0.977 0.3980 8.76
## 13 16 0.94000 -1.4500 0.931 0.682 0.2210 7.20
## 14 18 0.94400 -1.4200 0.933 0.500 0.1270 6.01
## 15 20 0.95500 -1.3900 0.955 0.380 0.0733 5.07
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8 9 10 11 12
## 119 25 25 20 18 18 16 16 12 12 11 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 13 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.## $magenta
## [1] "RRM2" "POLQ" "NCAPG2" "KIF11" "ECT2" "DIAPH3"
## [7] "ASPM" "KIF14" "NCAPG" "CDCA2" "DLGAP5" "HIST1H3B"
## [13] "HIST1H1B" "SPC25" "TPX2" "TOP2A" "BRCA2" "KIF15"
## [19] "CCDC150" "NUF2" "CDCA8" "FANCI" "STMN1" "TMPO"
## [25] "MKI67" "CIT" "HJURP" "NCAPH" "HIST1H4H" "KIF4A"
## [31] "HIST1H2AG" "INCENP" "HMGB2" "GTSE1" "KNL1" "AURKB"
## [37] "HIST1H2AH" "ANLN" "E2F2" "DDX11" "ZNF367" "CD99L2"
## [43] "KIFC1" "LINC00265" "CDK19" "RAD51" "ATAD5" "TACC3"
## [49] "RNF144B" "DEPDC1B" "E2F8" "MPC1" "WDR76" "MCM4"
## [55] "CENPP" "MED26" "INPP5F"
##
## $greenyellow
## [1] "MPP7" "SNX8" "ASPH" "ALAD" "MAN2B2" "TTC23L"
## [7] "BLK" "CLECL1" "EFL1" "SGO1-AS1"
##
## $turquoise
## [1] "PTMA" "RPS23" "RPS2" "RPL41" "RPS12"
## [6] "IL32" "RPS16" "TMSB10" "FAU" "RPS15"
## [11] "GAPDH" "ACTG1" "B2M" "RPL15" "CRIP1"
## [16] "RPL21" "RPS13" "AC079793.1" "PFN1" "S100A4"
## [21] "MZT2B" "VIM" "ACTB" "RPS11" "RPL38"
##
## $green
## [1] "ACO1" "AL606491.1" "TMEM63A" "DPH5" "AC079142.1"
## [6] "LIMK1" "ZBTB24" "HSF5" "FIRRE" "UBA6-AS1"
## [11] "TSPAN17" "CDRT4" "HCG17" "MRPS6" "SLX4IP"
## [16] "PRH1" "ENOX2" "CENPV" "ARHGEF3" "LRRC8D"
## [21] "COLQ" "ATG4C" "ALG14" "HAPLN3" "KCNMB4"
## [26] "C8orf37-AS1" "PPME1" "TMEM106B" "ZC3HC1" "SLC7A1"
##
## $black
## [1] "CCDC58" "PROK2" "FILNC1" "AC008549.2" "ZNF71"
## [6] "PAK1" "SDHAF3" "TTN-AS1" "FRY" "CCP110"
## [11] "AC017071.1" "ELOVL4" "PARL" "EPHB1" "LIPE-AS1"
## [16] "CRLS1" "AP002807.1" "PROSER3" "APAF1" "PGRMC2"
## [21] "AL365255.1" "ZKSCAN8" "PTPDC1" "B3GNT5" "C5orf17"
## [26] "PARD6B"
##
## $red
## [1] "TXNDC16" "RAI1" "NKG7" "AC017028.1" "TBRG4"
## [6] "MRPL20-AS1" "GUSB" "CDT1" "INSL6" "ERLIN1"
## [11] "UBE2A" "IFI44L" "AC004551.1" "POFUT1" "ASPN"
## [16] "L2HGDH"
##
## $purple
## [1] "AC092683.1" "TRIO" "ZNF549" "DYNC2LI1" "ANKMY2"
## [6] "UBE3C" "AL360270.1" "CD302" "NCDN" "MTHFS"
## [11] "NAB1"
##
## $yellow
## [1] "PPM1L" "FSD1L" "PDCD11" "ADCY3" "PHLPP2"
## [6] "AC068631.1" "WDR27" "CERS4" "CDK14" "ZBTB2"
## [11] "CHCHD6" "LINC00899" "EFCAB2" "ST7" "FBXL3"
## [16] "TSEN15" "DNM3" "INTU"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "10/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $magenta
## [1] "RRM2" "POLQ" "NCAPG2" "KIF11" "ECT2" "DIAPH3"
## [7] "ASPM" "KIF14" "NCAPG" "CDCA2" "DLGAP5" "HIST1H3B"
## [13] "HIST1H1B" "SPC25" "TPX2" "TOP2A" "BRCA2" "KIF15"
## [19] "CCDC150" "NUF2" "CDCA8" "FANCI" "STMN1" "TMPO"
## [25] "MKI67" "CIT" "HJURP" "NCAPH" "HIST1H4H" "KIF4A"
## [31] "HIST1H2AG" "INCENP" "HMGB2" "GTSE1" "KNL1" "AURKB"
## [37] "HIST1H2AH" "ANLN" "E2F2" "DDX11" "ZNF367" "CD99L2"
## [43] "KIFC1" "LINC00265" "CDK19" "RAD51" "ATAD5" "TACC3"
## [49] "RNF144B" "DEPDC1B" "E2F8" "MPC1" "WDR76" "MCM4"
## [55] "CENPP" "MED26" "INPP5F"
##
## $greenyellow
## [1] "MPP7" "SNX8" "ASPH" "ALAD" "MAN2B2" "TTC23L"
## [7] "BLK" "CLECL1" "EFL1" "SGO1-AS1"
##
## $turquoise
## [1] "PTMA" "RPS23" "RPS2" "RPL41" "RPS12"
## [6] "IL32" "RPS16" "TMSB10" "FAU" "RPS15"
## [11] "GAPDH" "ACTG1" "B2M" "RPL15" "CRIP1"
## [16] "RPL21" "RPS13" "AC079793.1" "PFN1" "S100A4"
## [21] "MZT2B" "VIM" "ACTB" "RPS11" "RPL38"
##
## $green
## [1] "ACO1" "AL606491.1" "TMEM63A" "DPH5" "AC079142.1"
## [6] "LIMK1" "ZBTB24" "HSF5" "FIRRE" "UBA6-AS1"
## [11] "TSPAN17" "CDRT4" "HCG17" "MRPS6" "SLX4IP"
## [16] "PRH1" "ENOX2" "CENPV" "ARHGEF3" "LRRC8D"
## [21] "COLQ" "ATG4C" "ALG14" "HAPLN3" "KCNMB4"
## [26] "C8orf37-AS1" "PPME1" "TMEM106B" "ZC3HC1" "SLC7A1"
##
## $black
## [1] "CCDC58" "PROK2" "FILNC1" "AC008549.2" "ZNF71"
## [6] "PAK1" "SDHAF3" "TTN-AS1" "FRY" "CCP110"
## [11] "AC017071.1" "ELOVL4" "PARL" "EPHB1" "LIPE-AS1"
## [16] "CRLS1" "AP002807.1" "PROSER3" "APAF1" "PGRMC2"
## [21] "AL365255.1" "ZKSCAN8" "PTPDC1" "B3GNT5" "C5orf17"
## [26] "PARD6B"
##
## $red
## [1] "TXNDC16" "RAI1" "NKG7" "AC017028.1" "TBRG4"
## [6] "MRPL20-AS1" "GUSB" "CDT1" "INSL6" "ERLIN1"
## [11] "UBE2A" "IFI44L" "AC004551.1" "POFUT1" "ASPN"
## [16] "L2HGDH"
##
## $purple
## [1] "AC092683.1" "TRIO" "ZNF549" "DYNC2LI1" "ANKMY2"
## [6] "UBE3C" "AL360270.1" "CD302" "NCDN" "MTHFS"
## [11] "NAB1"
##
## $yellow
## [1] "PPM1L" "FSD1L" "PDCD11" "ADCY3" "PHLPP2"
## [6] "AC068631.1" "WDR27" "CERS4" "CDK14" "ZBTB2"
## [11] "CHCHD6" "LINC00899" "EFCAB2" "ST7" "FBXL3"
## [16] "TSEN15" "DNM3" "INTU"
##
## [1] "Naltrexone_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.7594## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32006## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.3047e-30## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.
## PC_ 1
## Positive: BTBD9, GFPT1, FLI1, SLC16A7, CAPZA2, CMC2, AL136456.1, RAB3GAP1, AC008124.1, ZMYM2
## ZDHHC2, DCUN1D2, TTC13, AC005237.1, ATP13A3, ABLIM1, CNOT4, PPP2R5C, KIAA1109, SKAP1
## Negative: MTRNR2L8, RPL28, RPLP1, TMSB10, RPS23, RPL12, PTMA, RPL37A, RPL19, HIST1H4C
## TMSB4X, PFN1, RPS20, RPS15, RPS19, PCNA, RPL10, EEF1A1, EIF2B2, AC243829.2
## PC_ 2
## Positive: MALAT1, EPHA4, TSHZ2, ANK3, LDLRAD4, PVT1, SNX29, PRKCA, NOL4L, MGAT4A
## ZC3H12D, TTC39C, TRAF3IP2-AS1, ZMIZ1, ATP10A, AL138720.1, TAFA1, EEF2K, LINC02649, PIGZ
## Negative: ACTB, SH3BGRL3, TMSB10, EEF1A1, UBE2A, RPS15, RPS2, RPLP1, RPL41, RPL8
## CD52, RPS3, RPL36A, S100A4, TMSB4X, RPL28, RORA-AS1, RPS19, RPL37A, RPL37
## PC_ 3
## Positive: IL26, VWDE, ATP6V0A1, ERN1, CEP57, DMAC2L, P4HA1, CRADD, TMPRSS3, RORA
## PTPN13, SMIM12, FDX1, UBE2E3, IL18RAP, DEPDC5, FASTKD3, TC2N, EHBP1, IL12RB2
## Negative: PCAT1, PGM2L1, PTPN3, AC027018.1, SESTD1, AFF3, SESN3, NCOA1, UPP1, TIGIT
## CDRT4, CNR2, MIR4422HG, GFOD1, LYST, AC023906.5, STAU2, GPD2, GNAQ, AL157911.1
## PC_ 4
## Positive: BRIP1, AP001831.1, POLE, NLGN4Y, TRERF1, AC006206.2, GCNT2, NCAPG, FANCA, POLE2
## VAMP3, PLEKHG1, ITGB3BP, SPC25, WDR62, KNL1, SETD4, MTURN, COPG2, CEP295
## Negative: SMCO4, AC016831.1, AC009315.1, PKIA-AS1, ICA1, AC090825.1, AL592429.2, AC023790.2, CAMK2D, PIGU
## IL2RA, POU5F2, AL589693.1, AC005703.4, FRMD4A, BMT2, PITPNM2, TXK, AC131237.1, SAMD4A
## PC_ 5
## Positive: DTL, ZNF587B, GMNN, SKA2, SPC25, WDR62, CIT, ZNF367, ATAD5, PKD2
## AC093865.1, CATSPERE, CTSA, ST3GAL4, CSRNP2, SESTD1, FANCA, MAP3K20, KNL1, HIST1H4H
## Negative: ANK3, FAU, INPP4B, LIME1, CD226, TSHZ2, RPS23, PI4K2A, RABAC1, MIAT
## GCNT4, FAM24B, MAP3K1, PAG1, IL7R, LTB, AC079921.1, PCED1B, ST8SIA1, TMBIM4
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.34200 41.1000 0.188 208.000 208.0000 225.00
## 2 2 0.31500 19.2000 0.146 113.000 113.0000 133.00
## 3 3 0.47500 4.6800 0.651 63.300 63.1000 81.30
## 4 4 0.36100 2.6300 0.775 36.500 36.1000 51.50
## 5 5 0.26000 1.6900 0.815 21.700 21.4000 33.80
## 6 6 0.09760 0.8250 0.894 13.300 13.0000 23.00
## 7 7 0.00039 0.0425 0.860 8.480 8.2100 16.40
## 8 8 0.02070 -0.2500 0.831 5.560 5.3300 12.10
## 9 9 0.14700 -0.6190 0.800 3.770 3.4800 9.44
## 10 10 0.43500 -1.1500 0.828 2.630 2.3400 8.09
## 11 12 0.76700 -1.8700 0.801 1.400 1.1000 6.34
## 12 14 0.85700 -1.9600 0.842 0.830 0.5550 5.26
## 13 16 0.92200 -1.8500 0.921 0.539 0.2950 4.52
## 14 18 0.92800 -1.7300 0.914 0.378 0.1660 3.99
## 15 20 0.91800 -1.6200 0.895 0.282 0.0972 3.59
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4
## 353 11 10 10 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 4 module eigengenes in given set.## $yellow
## [1] "DMAC2L" "SMIM12" "IL12RB2" "C4orf48" "IFI44L" "CCDC112"
## [7] "PSAT1" "KEAP1" "CLIP1-AS1" "NIT2"
##
## $brown
## [1] "BRIP1" "POLE" "FANCA" "POLE2" "SPC25"
## [6] "WDR62" "KNL1" "COPG2" "GMNN" "CBX1"
## [11] "AC008770.3" "CIT" "ZNF367" "ATAD5" "MAP3K20"
## [16] "KNTC1" "DPH5" "AHDC1" "ZNF461" "KIAA1841"
## [21] "NAV1"
##
## $blue
## [1] "AC016831.1" "AC009315.1" "AL592429.2" "POU5F2" "AC093010.2"
## [6] "LINC02656" "TTYH2" "CLVS1" "FRG1-DT" "SFXN2"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $yellow
## [1] "DMAC2L" "SMIM12" "IL12RB2" "C4orf48" "IFI44L" "CCDC112"
## [7] "PSAT1" "KEAP1" "CLIP1-AS1" "NIT2"
##
## $brown
## [1] "BRIP1" "POLE" "FANCA" "POLE2" "SPC25"
## [6] "WDR62" "KNL1" "COPG2" "GMNN" "CBX1"
## [11] "AC008770.3" "CIT" "ZNF367" "ATAD5" "MAP3K20"
## [16] "KNTC1" "DPH5" "AHDC1" "ZNF461" "KIAA1841"
## [21] "NAV1"
##
## $blue
## [1] "AC016831.1" "AC009315.1" "AL592429.2" "POU5F2" "AC093010.2"
## [6] "LINC02656" "TTYH2" "CLVS1" "FRG1-DT" "SFXN2"
##
## [1] "Methadone_3"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.6521## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.31961## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 0## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## Error in irlba(A = t(x = object), nv = npcs, ...) :
## max(nu, nv) must be strictly less than min(nrow(A), ncol(A))
## [1] "Methadone_0"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : at -1.1302## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : radius 0.00026289## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : all data on boundary of neighborhood. make span bigger## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.1302## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.016214## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : zero-width neighborhood. make span bigger
## Error in irlba(A = t(x = object), nv = npcs, ...) :
## max(nu, nv) must be strictly less than min(nrow(A), ncol(A))saveRDS(mods1, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules_Treatment_Timepoint.rds")
#just doing treatment, we get at least 2 per condition
results.split<-SplitObject(results, "Treatment")
conds<-cbind(c(8, 7,6),c(6, 9,8))
mods2<-WrapGroupModID(results.split, "NA", conds)## [1] "Bup.Nalo"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.541## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.49964## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 6.0552e-16## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## PC_ 1
## Positive: ANK3, PCAT1, FAAH2, TTN, ABLIM1, DDX60L, MAML2, AL136456.1, PITPNC1, SESN3
## NEAT1, ZHX2, SORL1, PPP1R16B, XIST, FMN1, CMTM8, LEF1, UST, DLGAP1
## Negative: TUBA1B, TUBB, STMN1, HIST1H4C, RRM2, GAPDH, DIAPH3, TYMS, HMGB2, TK1
## HIST1H3B, PCLAF, FBXO5, HIST1H1B, TMPO, POLQ, NCAPG, NUSAP1, PFN1, PCNA
## PC_ 2
## Positive: RPL28, RPL41, RPL18A, RPL13A, RPL27A, RPS28, RPS19, RPS15, RPL11, RPS18
## RPS12, B2M, RPS27, RPL18, RPS23, RPS29, RPS2, RPS16, RPL37, RPLP1
## Negative: POLQ, NCAPG, CIT, KIF18B, DIAPH3, KIF15, ATAD5, SPC25, NCAPG2, BRCA2
## RRM2, KNTC1, BRIP1, DTL, NUSAP1, ASPM, KNL1, MKI67, CDCA2, TOP2A
## PC_ 3
## Positive: KIF14, KIF4A, PLK1, AURKA, LTB, UBE2C, NEAT1, HMMR, KIF20A, TSHZ2
## CCNF, SESN3, KIF23, CDCA2, CKAP2L, CDCA8, ASPM, SGO2, ESPL1, KIF18B
## Negative: PECAM1, MIR4422HG, PTPN3, LYST, NKG7, GZMK, AGAP1, KLRK1, MCTP2, DTHD1
## KCNQ5, AL031599.1, NCOA1, CNR2, UBE2E2, GZMA, SFMBT2, SESTD1, SLBP, AFF3
## PC_ 4
## Positive: MIR4422HG, PTPN3, DTHD1, PECAM1, UBE2E2, AL031599.1, LYST, SESTD1, GZMK, PACSIN1
## AFF3, PGM2L1, ANTXR2, RUNX2, LZTFL1, CBLB, CD38, CCNG2, BACH2, CENPA
## Negative: MSH6, FANCA, UHRF1, CLSPN, TRERF1, GPHN, EXO1, DTL, MPP6, NDUFAF6
## CDC45, MCOLN2, MCM4, PUS7, CCNE2, MCM10, ORC6, E2F7, HELLS, FKBP5
## PC_ 5
## Positive: PLCL1, STAM, TXK, CDHR3, AL136456.1, MGAT5, MAST4, ABLIM1, WDFY2, MCF2L2
## SNX29, SMYD3, ELP4, MGAT4A, ZC2HC1A, AL121935.1, ZNRF1, LINC01876, SNX9, CASK
## Negative: CCL5, NKG7, TGFBR3, TOP2A, CENPF, CDCA2, GZMH, HIST1H2BH, CD8B, GTSE1
## GZMA, KIF2C, AOAH, HIST1H3B, C1orf21, CCNB2, KIF14, PLK1, HIST2H2AA4, KLRD1
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00387 -0.524 0.3390 161.000 159.0000 179.00
## 2 2 0.20800 -1.900 0.4850 86.300 83.5000 110.00
## 3 3 0.60800 -2.430 0.7210 47.400 44.2000 70.60
## 4 4 0.68700 -2.150 0.7140 26.800 23.7000 47.80
## 5 5 0.77100 -2.060 0.7450 15.700 12.8000 33.80
## 6 6 0.82800 -1.900 0.7950 9.500 7.0800 24.80
## 7 7 0.79600 -1.680 0.7490 5.970 3.9000 18.70
## 8 8 0.82900 -1.540 0.7970 3.900 2.1900 14.50
## 9 9 0.78400 -1.460 0.7460 2.650 1.2300 11.40
## 10 10 0.70400 -1.390 0.6400 1.850 0.7070 9.13
## 11 12 0.20700 -2.560 0.1010 0.991 0.2440 6.05
## 12 14 0.20500 -2.230 0.1140 0.576 0.0916 4.17
## 13 16 0.21300 -2.110 0.1440 0.355 0.0353 2.94
## 14 18 0.79800 -1.110 0.7900 0.227 0.0159 2.11
## 15 20 0.19400 -1.890 0.0187 0.149 0.0066 1.54
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8 9 10 11
## 84 38 29 27 25 20 19 18 16 11 11 10
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 12 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 8 module eigengenes in given set.## $turquoise
## [1] "ANK3" "MAML2" "SORL1" "XIST" "FMN1" "GAPDH" "PFN1"
## [8] "ACTB" "RPL28" "RPL41" "RPL18A" "RPL13A" "RPL27A" "RPS28"
## [15] "RPS19" "RPS15" "RPL11" "RPS18" "RPS12" "B2M" "RPS27"
## [22] "RPL18" "RPS23" "RPS29" "RPS2" "RPS16" "RPL37" "RPLP1"
## [29] "RPL30" "RPL10" "RPS11" "RPS27A" "RPLP2" "LTB" "SNED1"
## [36] "ATP5F1E" "PLAC8" "RPS24"
##
## $greenyellow
## [1] "TTN" "SESN3" "LEF1" "PGM2L1" "AP000787.1"
## [6] "AC093865.1" "IKZF2" "FHIT" "RBMS3" "MAGI1"
##
## $pink
## [1] "ABLIM1" "AL136456.1" "NEAT1" "HMGN2" "H2AFZ"
## [6] "TSHZ2" "APOLD1" "ANTXR2" "RUNX2" "BACH2"
## [11] "PLCL1" "STAM" "CDHR3" "MGAT5" "MAST4"
## [16] "WDFY2" "SNX29" "SMYD3" "ELP4" "MGAT4A"
## [21] "AL121935.1" "SNX9" "CASK" "RFX3-AS1" "SAMD12"
## [26] "ARHGAP10" "ADK" "TROAP" "RORA" "PRKY"
## [31] "UTY" "IL2RA" "AL589693.1" "COL5A3" "USP9Y"
## [36] "CLIC5" "ANP32E" "NCALD" "CAMK2D" "LGMN"
## [41] "SGO1-AS1"
##
## $green
## [1] "TUBA1B" "TUBB" "STMN1" "HIST1H4C" "RRM2"
## [6] "DIAPH3" "HMGB2" "HIST1H3B" "FBXO5" "HIST1H1B"
## [11] "TMPO" "POLQ" "NCAPG" "NUSAP1" "MKI67"
## [16] "SMC2" "CIT" "KIF18B" "KIF15" "ATAD5"
## [21] "SPC25" "NCAPG2" "BRCA2" "KNTC1" "BRIP1"
## [26] "DTL" "ASPM" "KNL1" "CDCA2" "TOP2A"
## [31] "BUB1B" "ZGRF1" "CIP2A" "ANLN" "FANCA"
## [36] "KIF14" "KIF4A" "PLK1" "AURKA" "UBE2C"
## [41] "HMMR" "KIF20A" "CCNF" "KIF23" "CKAP2L"
## [46] "CDCA8" "SGO2" "ESPL1" "CCNB1" "INCENP"
## [51] "HIST2H2AA4" "SLBP" "CENPA" "MSH6" "UHRF1"
## [56] "CLSPN" "GPHN" "EXO1" "CDC45" "MCOLN2"
## [61] "MCM4" "PUS7" "CCNE2" "MCM10" "ORC6"
## [66] "E2F7" "HELLS" "FAM111B" "TBXAS1" "ECM2"
## [71] "CENPF" "HIST1H2BH" "GTSE1" "KIF2C" "CCNB2"
## [76] "HIST1H3D" "HIST1H3F" "HIST1H2AI" "SLC35A4" "JARID2"
## [81] "HSP90AA1" "DAD1" "CDC20" "CALM1" "ZWINT"
## [86] "DMC1" "CCDC34" "HIST1H2BO" "HMGA1" "HIST1H2BK"
## [91] "MAGI3" "MSC-AS1" "HIST1H3G" "DEPDC1" "PAICS"
##
## $magenta
## [1] "PECAM1" "MIR4422HG" "PTPN3" "LYST" "GZMK"
## [6] "AGAP1" "DTHD1" "AL031599.1" "UBE2E2" "GALNT1"
## [11] "CBLB"
##
## $black
## [1] "NKG7" "KLRK1" "GZMA" "CD8B" "MVB12B"
## [6] "TRERF1" "CCL5" "GZMH" "AOAH" "C1orf21"
## [11] "KLRD1" "ZEB2" "CTSW" "PPP2R2B" "PDGFD"
## [16] "MATK" "TRGC2" "AC022075.1"
##
## $purple
## [1] "AGPAT4" "GPR15" "SCMH1" "SYTL2" "IGF1R" "ZBTB16" "SELL" "ROR2"
## [9] "DEC1" "DOCK3" "PDE8A"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "8389/10000 permutations failed the Mann-Whitney test."
## [1] "7760/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "1831/10000 permutations failed the Mann-Whitney test."
## [1] "5387/10000 permutations failed the Mann-Whitney test."
## [1] "9466/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "ANK3" "MAML2" "SORL1" "XIST" "FMN1" "GAPDH" "PFN1"
## [8] "ACTB" "RPL28" "RPL41" "RPL18A" "RPL13A" "RPL27A" "RPS28"
## [15] "RPS19" "RPS15" "RPL11" "RPS18" "RPS12" "B2M" "RPS27"
## [22] "RPL18" "RPS23" "RPS29" "RPS2" "RPS16" "RPL37" "RPLP1"
## [29] "RPL30" "RPL10" "RPS11" "RPS27A" "RPLP2" "LTB" "SNED1"
## [36] "ATP5F1E" "PLAC8" "RPS24"
##
## $green
## [1] "TUBA1B" "TUBB" "STMN1" "HIST1H4C" "RRM2"
## [6] "DIAPH3" "HMGB2" "HIST1H3B" "FBXO5" "HIST1H1B"
## [11] "TMPO" "POLQ" "NCAPG" "NUSAP1" "MKI67"
## [16] "SMC2" "CIT" "KIF18B" "KIF15" "ATAD5"
## [21] "SPC25" "NCAPG2" "BRCA2" "KNTC1" "BRIP1"
## [26] "DTL" "ASPM" "KNL1" "CDCA2" "TOP2A"
## [31] "BUB1B" "ZGRF1" "CIP2A" "ANLN" "FANCA"
## [36] "KIF14" "KIF4A" "PLK1" "AURKA" "UBE2C"
## [41] "HMMR" "KIF20A" "CCNF" "KIF23" "CKAP2L"
## [46] "CDCA8" "SGO2" "ESPL1" "CCNB1" "INCENP"
## [51] "HIST2H2AA4" "SLBP" "CENPA" "MSH6" "UHRF1"
## [56] "CLSPN" "GPHN" "EXO1" "CDC45" "MCOLN2"
## [61] "MCM4" "PUS7" "CCNE2" "MCM10" "ORC6"
## [66] "E2F7" "HELLS" "FAM111B" "TBXAS1" "ECM2"
## [71] "CENPF" "HIST1H2BH" "GTSE1" "KIF2C" "CCNB2"
## [76] "HIST1H3D" "HIST1H3F" "HIST1H2AI" "SLC35A4" "JARID2"
## [81] "HSP90AA1" "DAD1" "CDC20" "CALM1" "ZWINT"
## [86] "DMC1" "CCDC34" "HIST1H2BO" "HMGA1" "HIST1H2BK"
## [91] "MAGI3" "MSC-AS1" "HIST1H3G" "DEPDC1" "PAICS"
##
## [1] "Naltrexone"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.1607## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32185## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 2.7607e-31## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619
## PC_ 1
## Positive: NCAPG2, DIAPH3, NCAPG, KIF14, POLQ, RRM2, SPC25, ATAD5, TOP2A, CCDC150
## BRCA2, E2F8, BARD1, LMNB1, KIF11, HIST1H3B, RUNX1, CENPK, CDCA2, CDCA8
## Negative: MTRNR2L8, JUN, AFF3, AC243829.2, ZNF331, PGAM5, RBFOX3, JUNB, AC137810.1, RBMS3
## KCNQ1OT1, EFCAB8, AC105402.3, RILPL2, CCDC102B, RPS19, GRIK1, DEC1, RAP2C-AS1, LINC01505
## PC_ 2
## Positive: KIF11, DIAPH3, RRM2, POLQ, ASPM, HIST1H3B, KIF14, CDCA8, NCAPG, FANCI
## STIL, SPC25, TPX2, HIST1H1B, HIST1H4H, DLGAP5, SHCBP1, CIT, INCENP, NUSAP1
## Negative: ZBTB20, ANK3, TSHZ2, KLF12, CD28, TC2N, RFX3, CELF2, PRKCA, SERINC5
## ABLIM1, ARID1B, RNASET2, EPHA4, GABPB1-AS1, CAMKMT, INPP4B, ACYP2, TSPOAP1-AS1, MAML2
## PC_ 3
## Positive: DTHD1, SESTD1, CEP128, LDLRAD4, PTPN3, MIR4422HG, AFF3, E2F3, AGAP1, TRPS1
## FOXP1, TTN, TXK, BCL2, PCAT1, MYB, HAVCR2, PECAM1, SOS2, CNR2
## Negative: RPS2, CD52, IL32, RPL41, RPS19, RPS16, CRIP1, FAU, LTB, TMSB10
## RPS15, S100A4, ACTG1, GAPDH, RPS28, RPL23, ACTB, LINC02694, RPS13, ATP5PF
## PC_ 4
## Positive: PTPN3, SESTD1, MCTP2, AFF3, UBE2E2, PCAT1, RPS15, LYST, MIR4422HG, PGM2L1
## CNR2, PECAM1, RPL41, RPS2, TIGIT, AC104078.2, ANTXR2, DTHD1, TMSB10, AC093019.2
## Negative: TTC39C, RORA, PTPN13, AL136456.1, FRY, FLI1, IL18R1, GRAMD1B, LINC00299, ERN1
## ADAM19, HIVEP3, MAP3K1, SAMD8, RPS6KA3, EGLN3, TC2N, TMPRSS3, PAG1, ETV6
## PC_ 5
## Positive: MALAT1, INPP4B, JUNB, TSHZ2, IMMP2L, MPP7, ANK3, TNFAIP3, FOS, UST
## FOSB, RGCC, ST6GALNAC3, DISC1, AP000787.1, RNASET2, CCR7, SNED1, TUBB4B, HIST1H3F
## Negative: USP18, NKG7, GZMA, HLA-DQA2, AC017028.1, INSL6, RHEBL1, MRPL20-AS1, IL18RAP, GOLIM4
## AC004551.1, CDT1, ATG16L2, FECH, ARHGEF7, CCL5, TMPRSS3, IL26, HLA-DRB1, RPTOR
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.5730 24.50 0.91000 154.000 154.0000 161.00
## 2 2 0.1560 4.89 0.70100 81.000 80.9000 91.40
## 3 3 0.0339 -1.12 0.76900 43.500 43.2000 55.10
## 4 4 0.2810 -2.33 0.56000 24.000 23.5000 35.60
## 5 5 0.4800 -2.60 0.50600 13.600 13.0000 24.50
## 6 6 0.5990 -2.29 0.53300 7.950 7.3500 17.90
## 7 7 0.6620 -2.10 0.56900 4.830 4.1400 13.80
## 8 8 0.7620 -2.06 0.69500 3.060 2.3900 11.00
## 9 9 0.8450 -1.96 0.81500 2.020 1.4300 9.00
## 10 10 0.8190 -1.80 0.79700 1.390 0.8690 7.57
## 11 12 0.9090 -1.54 0.89100 0.733 0.3350 5.56
## 12 14 0.8830 -1.40 0.85800 0.438 0.1400 4.19
## 13 16 0.8810 -1.30 0.85300 0.286 0.0627 3.21
## 14 18 0.8630 -1.25 0.82500 0.198 0.0298 2.48
## 15 20 0.2060 -2.00 0.00753 0.143 0.0143 1.94
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5
## 213 26 19 14 14 12
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 6 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.## $green
## [1] "NCAPG2" "DIAPH3" "NCAPG" "KIF14" "POLQ" "RRM2"
## [7] "SPC25" "ATAD5" "TOP2A" "CCDC150" "BRCA2" "E2F8"
## [13] "BARD1" "LMNB1" "KIF11" "HIST1H3B" "CENPK" "CDCA2"
## [19] "CDCA8" "FANCI" "CCNF" "ASPM" "CIP2A" "STIL"
## [25] "TPX2" "HIST1H1B" "HIST1H4H" "DLGAP5" "SHCBP1" "CIT"
## [31] "INCENP" "NUSAP1" "HIST1H2AH" "KNL1" "KIF4A" "ANLN"
## [37] "HIST1H3F" "RFC3"
##
## $brown
## [1] "AFF3" "DTHD1" "SESTD1" "PTPN3" "MIR4422HG" "MYB"
## [7] "HAVCR2" "PECAM1" "LINC02320" "HAVCR1" "MCTP2" "UBE2E2"
## [13] "LYST" "TIGIT"
##
## $blue
## [1] "RPS19" "RPS2" "CD52" "IL32" "RPL41" "RPS16" "CRIP1" "FAU"
## [9] "LTB" "TMSB10" "RPS15" "S100A4" "ACTG1" "GAPDH" "RPS28" "RPL23"
## [17] "ACTB" "RPS13" "S100A6"
##
## $yellow
## [1] "ATP5PF" "USP18" "HLA-DQA2" "AC017028.1" "INSL6"
## [6] "RHEBL1" "MRPL20-AS1" "GOLIM4" "AC004551.1" "CDT1"
## [11] "HLA-DRB1" "IFI6" "C2orf92" "TRIM21"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $green
## [1] "NCAPG2" "DIAPH3" "NCAPG" "KIF14" "POLQ" "RRM2"
## [7] "SPC25" "ATAD5" "TOP2A" "CCDC150" "BRCA2" "E2F8"
## [13] "BARD1" "LMNB1" "KIF11" "HIST1H3B" "CENPK" "CDCA2"
## [19] "CDCA8" "FANCI" "CCNF" "ASPM" "CIP2A" "STIL"
## [25] "TPX2" "HIST1H1B" "HIST1H4H" "DLGAP5" "SHCBP1" "CIT"
## [31] "INCENP" "NUSAP1" "HIST1H2AH" "KNL1" "KIF4A" "ANLN"
## [37] "HIST1H3F" "RFC3"
##
## $brown
## [1] "AFF3" "DTHD1" "SESTD1" "PTPN3" "MIR4422HG" "MYB"
## [7] "HAVCR2" "PECAM1" "LINC02320" "HAVCR1" "MCTP2" "UBE2E2"
## [13] "LYST" "TIGIT"
##
## $blue
## [1] "RPS19" "RPS2" "CD52" "IL32" "RPL41" "RPS16" "CRIP1" "FAU"
## [9] "LTB" "TMSB10" "RPS15" "S100A4" "ACTG1" "GAPDH" "RPS28" "RPL23"
## [17] "ACTB" "RPS13" "S100A6"
##
## $yellow
## [1] "ATP5PF" "USP18" "HLA-DQA2" "AC017028.1" "INSL6"
## [6] "RHEBL1" "MRPL20-AS1" "GOLIM4" "AC004551.1" "CDT1"
## [11] "HLA-DRB1" "IFI6" "C2orf92" "TRIM21"
##
## [1] "Methadone"## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -1.7674## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.32024## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 1.9936e-30## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : There are other near singularities as well. 0.090619## Warning in irlba(A = t(x = object), nv = npcs, ...): You're computing too large
## a percentage of total singular values, use a standard svd instead.
## PC_ 1
## Positive: KIF11, TUBA1B, MND1, HIST1H2AH, MRPL18, CCNF, AURKB, EIF4A3, KIF23, UBE2C
## HIST1H2BD, PGAM1, CDCA2, KIF15, ARL2, CCNA2, HIST1H2BB, SKA1, HIST1H3G, HIST2H4B
## Negative: ANK3, LINC00278, BCL2, CWC25, SATB1-AS1, MGAT4A, EGLN3, CCR6, RALGPS2, ZBTB20
## LINC01876, TTC39C, ABAT, RETREG1, PRKCA, SLC25A13, CYTH3, TSPAN3, TANC2, SLC4A5
## PC_ 2
## Positive: RPL13A, RPL19, RPS12, RPS23, RPL28, RPS18, RPLP2, RPS27, RPS17, RPS28
## RPS21, RPL9, RPS16, RPL37A, RPS15, RPL41, RPL23A, RPL18A, RPL36A, RPL35
## Negative: TBCEL, HDAC1, RORA, IFNAR2, INPP5F, GRAMD1B, DENND1A, SUCLA2, MAP2K6, NHEJ1
## KIF16B, RASA1, HECA, SERINC5, CAMKMT, RIPOR2, PHF21A, MARCH3, TCEANC2, SULT1B1
## PC_ 3
## Positive: PSMB4, CDK1, HIST1H3G, CDCA8, CDC20, HIST1H2BB, JAKMIP1, DEPDC1B, CCNB1, CDON
## KIF23, UBE2C, CCNB2, HIST1H3B, CDCA2, ARL2, CCNA2, SKA1, HIST1H3F, PLK2
## Negative: FANCB, LIN52, ADD3-AS1, PXMP2, FANCA, HELLS, CSTF2, LINC00871, URB1, GPATCH4
## C15orf41, ATAD2, ZGRF1, BRIP1, CHROMR, CENPU, XRCC2, XYLB, POLE2, IPPK
## PC_ 4
## Positive: RPL36A, ZNF177, TMSB10, RPL38, RPS15A, LYRM7, GAPDH, RPS2, MYL6, RPL18A
## RPL37A, TMSB4X, TESK2, KCNMB4, RPL41, PARK7, CIAO2A, DNM3, EEF1G, RPS24
## Negative: TTK, EFCAB5, TPX2, NCAPG, HJURP, STIL, KIF4A, E2F8, OGN, ASPM
## RAD51AP1, CENPA, KIF18B, AC003093.1, ERH, HIST1H2AL, CDCA5, P4HB, CDON, CCNB1
## PC_ 5
## Positive: BCAS4, ZC3H12B, CCL28, TMEM72-AS1, UST, TXNDC12, SEC22C, RFESD, MAP3K7CL, SPIN3
## ACER3, DIRC3, IGSF9B, C5orf17, EPHA4, CLDN12, FHIT, RHBDD1, AC233976.1, LRRN3
## Negative: TCEANC2, ANTXR2, CLCN3, SEPTIN8, RRM2B, GDAP1, AUTS2, CNDP2, SAMD3, AC107223.1
## AL162493.1, GABPB1, POMK, AL080250.1, AL138778.1, DDX10, TP63, B4GALT5, TNFRSF19, HOMER2
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 2.69e-01 4.8700 0.8230 143.00 143.000 162.0
## 2 2 9.82e-02 1.5000 0.4690 81.60 79.900 105.0
## 3 3 2.73e-05 -0.0141 0.1190 48.80 46.300 73.2
## 4 4 1.13e-01 -0.6200 0.0367 30.80 28.200 55.1
## 5 5 3.74e-01 -0.9590 0.2290 20.50 17.900 45.0
## 6 6 5.53e-01 -1.1400 0.4250 14.50 11.600 38.7
## 7 7 6.16e-01 -1.2600 0.5200 10.80 7.810 34.5
## 8 8 6.93e-01 -1.2600 0.6640 8.40 5.570 31.7
## 9 9 6.46e-01 -1.2600 0.6420 6.81 4.010 29.6
## 10 10 6.45e-01 -1.2100 0.6590 5.70 2.990 27.9
## 11 12 6.20e-01 -1.1300 0.7800 4.30 1.780 25.6
## 12 14 6.82e-01 -1.0800 0.8520 3.48 1.080 23.8
## 13 16 6.02e-01 -1.0600 0.7670 2.94 0.678 22.5
## 14 18 6.99e-01 -0.9930 0.8560 2.57 0.441 21.3
## 15 20 6.46e-01 -0.9690 0.8030 2.29 0.291 20.3
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8 9
## 44 48 37 34 22 19 18 16 15 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 10 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## $turquoise
## [1] "KIF11" "TUBA1B" "MND1" "HIST1H2AH" "MRPL18" "CCNF"
## [7] "AURKB" "EIF4A3" "KIF23" "UBE2C" "HIST1H2BD" "PGAM1"
## [13] "CDCA2" "KIF15" "ARL2" "CCNA2" "HIST1H2BB" "SKA1"
## [19] "HIST1H3G" "HIST2H4B" "CDK1" "HMMR" "PLK2" "TMEM60"
## [25] "HIST1H2AM" "PSMB4" "CDCA8" "CDC20" "JAKMIP1" "DEPDC1B"
## [31] "CCNB1" "CDON" "CCNB2" "HIST1H3B" "HIST1H3F" "C21orf58"
## [37] "CCDC34" "TTK" "TPX2" "NCAPG" "HJURP" "ASPM"
## [43] "RAD51AP1" "CENPA" "KIF18B" "HIST1H2AL" "P4HB" "NCAPH"
##
## $brown
## [1] "ANK3" "BCL2" "RALGPS2" "ZBTB20" "RETREG1"
## [6] "PRKCA" "CYTH3" "TANC2" "FOXP1" "KIF16B"
## [11] "MARCH3" "BCAS4" "ZC3H12B" "CCL28" "TMEM72-AS1"
## [16] "UST" "TXNDC12" "SEC22C" "RFESD" "MAP3K7CL"
## [21] "SPIN3" "DIRC3" "IGSF9B" "C5orf17" "EPHA4"
## [26] "CLDN12" "FHIT" "RHBDD1" "AC233976.1" "LRRN3"
## [31] "LEF1-AS1" "ADAM22" "HS1BP3" "AC092650.1"
##
## $black
## [1] "MGAT4A" "TBCEL" "RORA" "INPP5F" "GRAMD1B" "SUCLA2" "RASA1"
## [8] "HECA" "SERINC5" "CAMKMT" "RIPOR2" "PHF21A" "R3HDM1" "TXK"
## [15] "MIATNB" "DPP8"
##
## $blue
## [1] "RPL13A" "RPL19" "RPS12" "RPS23" "RPL28"
## [6] "RPS18" "RPLP2" "RPS27" "RPS17" "RPS28"
## [11] "RPS21" "RPL9" "RPS16" "RPL37A" "RPS15"
## [16] "RPL41" "RPL23A" "RPL18A" "RPL36A" "RPL35"
## [21] "RACK1" "RPS24" "SERF2" "ACTG1" "TMSB10"
## [26] "RPL38" "RPS15A" "GAPDH" "RPS2" "MYL6"
## [31] "TMSB4X" "PARK7" "EEF1G" "LTB" "AC079793.1"
## [36] "RPL11" "RPL23"
##
## $magenta
## [1] "RPS4X" "FANCA" "CSTF2" "LINC00871" "C15orf41" "XRCC2"
## [7] "DPF3" "TESK2" "HDGF" "STAM" "CD109"
##
## $yellow
## [1] "NHEJ1" "TCEANC2" "CLCN3" "AC073529.1" "ANTXR2"
## [6] "SEPTIN8" "RRM2B" "GDAP1" "CNDP2" "AC107223.1"
## [11] "AL162493.1" "POMK" "AL080250.1" "AL138778.1" "TP63"
## [16] "TNFRSF19" "HOMER2" "UTP25" "AFG1L" "AC022893.1"
## [21] "SLC19A2" "ALDH3A2"
##
## $green
## [1] "FANCB" "LIN52" "ADD3-AS1" "PXMP2" "HELLS"
## [6] "URB1" "ATAD2" "ZGRF1" "BRIP1" "CHROMR"
## [11] "CENPU" "XYLB" "NT5DC3" "ZNF519" "DNA2"
## [16] "EFCAB5" "STIL" "KIF4A" "E2F8" "OGN"
## [21] "AC003093.1" "ERH" "CDCA5" "DDX10" "PHF7"
## [26] "MPLKIP" "CYP7B1" "CDK14" "RAB33B" "GINS4"
## [31] "AC104806.2" "CARNMT1" "CYSLTR1" "HLF"
##
## $red
## [1] "GPATCH4" "IPPK" "FADD" "LIX1L-AS1" "SUCLG2-AS1"
## [6] "SHMT2" "NSMCE1" "PRDX4" "SCN8A" "PRMT1"
## [11] "PRDX2" "FOSL2" "AOAH" "PTPN22" "MAP3K9"
## [16] "GSTP1" "UBE2T" "IL5RA"
##
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "23/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "469/10000 permutations failed the Mann-Whitney test."
## [1] "56/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $turquoise
## [1] "KIF11" "TUBA1B" "MND1" "HIST1H2AH" "MRPL18" "CCNF"
## [7] "AURKB" "EIF4A3" "KIF23" "UBE2C" "HIST1H2BD" "PGAM1"
## [13] "CDCA2" "KIF15" "ARL2" "CCNA2" "HIST1H2BB" "SKA1"
## [19] "HIST1H3G" "HIST2H4B" "CDK1" "HMMR" "PLK2" "TMEM60"
## [25] "HIST1H2AM" "PSMB4" "CDCA8" "CDC20" "JAKMIP1" "DEPDC1B"
## [31] "CCNB1" "CDON" "CCNB2" "HIST1H3B" "HIST1H3F" "C21orf58"
## [37] "CCDC34" "TTK" "TPX2" "NCAPG" "HJURP" "ASPM"
## [43] "RAD51AP1" "CENPA" "KIF18B" "HIST1H2AL" "P4HB" "NCAPH"
##
## $brown
## [1] "ANK3" "BCL2" "RALGPS2" "ZBTB20" "RETREG1"
## [6] "PRKCA" "CYTH3" "TANC2" "FOXP1" "KIF16B"
## [11] "MARCH3" "BCAS4" "ZC3H12B" "CCL28" "TMEM72-AS1"
## [16] "UST" "TXNDC12" "SEC22C" "RFESD" "MAP3K7CL"
## [21] "SPIN3" "DIRC3" "IGSF9B" "C5orf17" "EPHA4"
## [26] "CLDN12" "FHIT" "RHBDD1" "AC233976.1" "LRRN3"
## [31] "LEF1-AS1" "ADAM22" "HS1BP3" "AC092650.1"
##
## $black
## [1] "MGAT4A" "TBCEL" "RORA" "INPP5F" "GRAMD1B" "SUCLA2" "RASA1"
## [8] "HECA" "SERINC5" "CAMKMT" "RIPOR2" "PHF21A" "R3HDM1" "TXK"
## [15] "MIATNB" "DPP8"
##
## $blue
## [1] "RPL13A" "RPL19" "RPS12" "RPS23" "RPL28"
## [6] "RPS18" "RPLP2" "RPS27" "RPS17" "RPS28"
## [11] "RPS21" "RPL9" "RPS16" "RPL37A" "RPS15"
## [16] "RPL41" "RPL23A" "RPL18A" "RPL36A" "RPL35"
## [21] "RACK1" "RPS24" "SERF2" "ACTG1" "TMSB10"
## [26] "RPL38" "RPS15A" "GAPDH" "RPS2" "MYL6"
## [31] "TMSB4X" "PARK7" "EEF1G" "LTB" "AC079793.1"
## [36] "RPL11" "RPL23"
##
## $magenta
## [1] "RPS4X" "FANCA" "CSTF2" "LINC00871" "C15orf41" "XRCC2"
## [7] "DPF3" "TESK2" "HDGF" "STAM" "CD109"
##
## $yellow
## [1] "NHEJ1" "TCEANC2" "CLCN3" "AC073529.1" "ANTXR2"
## [6] "SEPTIN8" "RRM2B" "GDAP1" "CNDP2" "AC107223.1"
## [11] "AL162493.1" "POMK" "AL080250.1" "AL138778.1" "TP63"
## [16] "TNFRSF19" "HOMER2" "UTP25" "AFG1L" "AC022893.1"
## [21] "SLC19A2" "ALDH3A2"
##
## $green
## [1] "FANCB" "LIN52" "ADD3-AS1" "PXMP2" "HELLS"
## [6] "URB1" "ATAD2" "ZGRF1" "BRIP1" "CHROMR"
## [11] "CENPU" "XYLB" "NT5DC3" "ZNF519" "DNA2"
## [16] "EFCAB5" "STIL" "KIF4A" "E2F8" "OGN"
## [21] "AC003093.1" "ERH" "CDCA5" "DDX10" "PHF7"
## [26] "MPLKIP" "CYP7B1" "CDK14" "RAB33B" "GINS4"
## [31] "AC104806.2" "CARNMT1" "CYSLTR1" "HLF"
##
## $red
## [1] "GPATCH4" "IPPK" "FADD" "LIX1L-AS1" "SUCLG2-AS1"
## [6] "SHMT2" "NSMCE1" "PRDX4" "SCN8A" "PRMT1"
## [11] "PRDX2" "FOSL2" "AOAH" "PTPN22" "MAP3K9"
## [16] "GSTP1" "UBE2T" "IL5RA"saveRDS(mods2, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules_Treatment.rds")
#finally looking at all proliferating cells to see if we can find something interesting, just got 2 out of it
mods3<-ModID(results, nPCS = 9, softpower = 6)## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : pseudoinverse used at -2.4183## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : neighborhood radius 0.30103## Warning in simpleLoess(y, x, w, span, degree = degree, parametric = parametric,
## : reciprocal condition number 9.8548e-16## PC_ 1
## Positive: ANK3, TSHZ2, ZBTB20, FAAH2, MAML2, PRKCA, LDLRAD4, PCAT1, ABLIM1, TTN
## MGAT4A, C22orf34, UST, AL136456.1, PFKFB3, TAFA1, SESN3, MPP7, LINC01422, AL353660.1
## Negative: TUBA1B, TUBB, HIST1H4C, GAPDH, RRM2, STMN1, DIAPH3, ACTB, PFN1, HIST1H3B
## POLQ, TYMS, NCAPG, TK1, HIST1H2AH, TMPO, PCLAF, HIST1H1B, CFL1, HMGN2
## PC_ 2
## Positive: POLQ, NCAPG, DIAPH3, SPC25, CIT, KIF18B, KIF15, RRM2, ASPM, ATAD5
## NCAPG2, CDCA2, NUSAP1, KIF11, KIF14, TOP2A, KNL1, BUB1B, KIF4A, BRIP1
## Negative: RPL28, RPL18A, RPL41, RPS15, RPL27A, RPL13A, RPS28, RPS19, RPL11, RPS12
## RPS23, RPS29, RPS18, RPS27, RPL10, RPL18, RPL37, RPS16, B2M, RPLP1
## PC_ 3
## Positive: ABLIM1, ZBTB20, MGAT5, MAP3K1, RORA, WDFY2, SSBP2, MAP3K4, RFX3, MCF2L2
## TSHZ2, ARL15, AL136456.1, DUSP16, AKT3, ATP13A3, PHF21A, UST, MAST4, PRKCA
## Negative: MTRNR2L8, NKG7, AGAP1, PECAM1, CCL5, GZMA, MKI67, CD8A, CENPF, HMGB2
## KLRK1, CD8B, AOAH, ZEB2, KPNA2, NAALADL2, TOP2A, HIST1H1E, HSP90B1, INCENP
## PC_ 4
## Positive: PTPN3, MIR4422HG, PECAM1, DTHD1, LYST, SESTD1, GZMK, NCOA1, MCTP2, CNR2
## HAVCR2, AL031599.1, UBE2E2, AGAP1, AFF3, KLRK1, ANTXR2, TRPS1, SAMD3, RPTOR
## Negative: LTB, SORL1, MAP3K1, ANK3, TTC39C, KIF14, TSHZ2, CDCA2, KIF4A, CKAP2L
## KIF2C, TNFAIP3, CDCA8, JUNB, UBE2C, ESPL1, RPS19, EPHA4, FMN1, SGO2
## PC_ 5
## Positive: DTL, MSH6, CLSPN, TRERF1, EXO1, CDC45, FANCA, MCM4, CDC6, CCNE2
## CTSW, HELLS, CCL5, ZEB2, POLE2, MCOLN2, C1orf21, MTHFD1L, FAM111B, THEMIS
## Negative: SESN3, SESTD1, MIR4422HG, KIF14, PTPN3, LDLRAD4, PLK1, KIF20A, KIF23, AFF3
## KIF4A, HMMR, BACH2, AURKB, TXK, DTHD1, CCNB2, APOLD1, AURKA, CDCA8
## Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k.
## 1 1 0.00548 -0.71 0.359 174.000 1.73e+02 194.00
## 2 2 0.31800 -2.72 0.415 93.800 9.08e+01 120.00
## 3 3 0.56700 -2.90 0.564 51.700 4.81e+01 77.10
## 4 4 0.68100 -2.40 0.666 29.200 2.55e+01 51.90
## 5 5 0.63700 -2.34 0.611 17.000 1.38e+01 36.40
## 6 6 0.69700 -2.04 0.660 10.200 7.62e+00 26.40
## 7 7 0.67700 -1.88 0.651 6.380 4.18e+00 19.70
## 8 8 0.68000 -1.70 0.635 4.120 2.32e+00 15.10
## 9 9 0.22600 -3.56 0.120 2.750 1.30e+00 11.70
## 10 10 0.22600 -3.15 0.132 1.900 7.36e-01 9.26
## 11 12 0.21700 -2.64 0.131 0.986 2.50e-01 5.97
## 12 14 0.21100 -2.31 0.120 0.557 8.78e-02 3.98
## 13 16 0.21300 -2.17 0.119 0.335 3.52e-02 2.72
## 14 18 0.79800 -1.11 0.782 0.210 1.38e-02 1.89
## 15 20 0.78800 -1.07 0.746 0.135 5.59e-03 1.33
## TOM calculation: adjacency..
## ..will not use multithreading.
## Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.
## dynamicMods
## 0 1 2 3 4 5 6 7 8
## 135 48 37 31 24 19 14 12 11
## mergeCloseModules: Merging modules whose distance is less than 0.5
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 9 module eigengenes in given set.
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## Calculating new MEs...
## multiSetMEs: Calculating module MEs.
## Working on set 1 ...
## moduleEigengenes: Calculating 5 module eigengenes in given set.
## $red
## [1] "TSHZ2" "ABLIM1" "AL136456.1" "LINC01876" "MGAT5"
## [6] "RORA" "MAP3K4" "DUSP16" "PHF21A" "MAST4"
## [11] "NEAT1" "CDHR3" "AL589693.1" "PLCL1"
##
## $yellow
## [1] "PCAT1" "AGAP1" "PECAM1" "PTPN3" "MIR4422HG"
## [6] "DTHD1" "LYST" "SESTD1" "GZMK" "NCOA1"
## [11] "MCTP2" "CNR2" "HAVCR2" "AL031599.1" "UBE2E2"
## [16] "AFF3" "ANTXR2" "TRPS1" "SAMD3" "AC104078.2"
## [21] "MYB" "GFOD1" "KCNQ5" "CD38"
##
## $brown
## [1] "TUBA1B" "TUBB" "HIST1H4C" "RRM2" "STMN1"
## [6] "DIAPH3" "HIST1H3B" "POLQ" "NCAPG" "HIST1H2AH"
## [11] "TMPO" "PCLAF" "HIST1H1B" "PCNA" "FBXO5"
## [16] "ASPM" "SPC25" "CIT" "KIF18B" "KIF15"
## [21] "ATAD5" "NCAPG2" "CDCA2" "NUSAP1" "KIF11"
## [26] "KIF14" "TOP2A" "KNL1" "BUB1B" "KIF4A"
## [31] "BRIP1" "CIP2A" "BRCA2" "ECT2" "FANCI"
## [36] "MKI67" "ATP13A3" "CENPF" "HMGB2" "KPNA2"
## [41] "HIST1H1E" "HSP90B1" "INCENP" "HSP90AA1" "CKAP2L"
## [46] "KIF2C" "CDCA8" "UBE2C" "ESPL1" "SGO2"
## [51] "KIF23" "PLK1" "CCNF" "DTL" "MSH6"
## [56] "CLSPN" "EXO1" "CDC45" "FANCA" "MCM4"
## [61] "CDC6" "CCNE2" "HELLS" "POLE2" "MTHFD1L"
## [66] "FAM111B" "MPP6" "HNRNPAB" "CENPP" "FANCC"
## [71] "KIF20A" "HMMR" "AURKB" "CCNB2" "APOLD1"
## [76] "AURKA" "CENPA" "CCNB1" "SCMH1" "C12orf75"
## [81] "DMC1" "MCM5" "FEN1" "MCM7" "MCM10"
## [86] "RRM1" "MIR4435-2HG" "LGMN" "IL2RA" "KNTC1"
## [91] "F5" "ADTRP" "SELL" "KHDC1" "HIST1H3G"
## [96] "HIST1H3F" "HIST1H2BH" "HIST1H3D" "CHTF18" "HIST1H2BF"
## [101] "HIST1H2AL" "CKS1B" "HIST1H2AI" "HIST1H2AG" "HIST2H4B"
## [106] "HIST1H2BB" "HIST1H3C" "SBF2" "CENPS"
##
## $black
## [1] "GAPDH" "ACTB" "PFN1" "CFL1" "ACTG1"
## [6] "RPL28" "RPL18A" "RPL41" "RPS15" "RPL27A"
## [11] "RPL13A" "RPS28" "RPS19" "RPL11" "RPS12"
## [16] "RPS23" "RPS29" "RPS18" "RPS27" "RPL10"
## [21] "RPL18" "RPL37" "RPS16" "B2M" "RPLP1"
## [26] "RPS2" "RPS27A" "RPL37A" "RPS15A" "RPLP2"
## [31] "PTMA" "LTB" "JUNB" "SCD5" "SPON1"
## [36] "ANXA2" "DAD1" "AC022075.1" "NDUFA6" "FKBP1A"
## [41] "PKM" "BCAT1" "FABP5" "NUTF2" "LSM5"
## [46] "PRDX1" "ATP5F1E" "TMSB10" "RPS24"
##
## [1] "9485/10000 permutations failed the Mann-Whitney test."
## [1] "5647/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## [1] "0/10000 permutations failed the Mann-Whitney test."
## $brown
## [1] "TUBA1B" "TUBB" "HIST1H4C" "RRM2" "STMN1"
## [6] "DIAPH3" "HIST1H3B" "POLQ" "NCAPG" "HIST1H2AH"
## [11] "TMPO" "PCLAF" "HIST1H1B" "PCNA" "FBXO5"
## [16] "ASPM" "SPC25" "CIT" "KIF18B" "KIF15"
## [21] "ATAD5" "NCAPG2" "CDCA2" "NUSAP1" "KIF11"
## [26] "KIF14" "TOP2A" "KNL1" "BUB1B" "KIF4A"
## [31] "BRIP1" "CIP2A" "BRCA2" "ECT2" "FANCI"
## [36] "MKI67" "ATP13A3" "CENPF" "HMGB2" "KPNA2"
## [41] "HIST1H1E" "HSP90B1" "INCENP" "HSP90AA1" "CKAP2L"
## [46] "KIF2C" "CDCA8" "UBE2C" "ESPL1" "SGO2"
## [51] "KIF23" "PLK1" "CCNF" "DTL" "MSH6"
## [56] "CLSPN" "EXO1" "CDC45" "FANCA" "MCM4"
## [61] "CDC6" "CCNE2" "HELLS" "POLE2" "MTHFD1L"
## [66] "FAM111B" "MPP6" "HNRNPAB" "CENPP" "FANCC"
## [71] "KIF20A" "HMMR" "AURKB" "CCNB2" "APOLD1"
## [76] "AURKA" "CENPA" "CCNB1" "SCMH1" "C12orf75"
## [81] "DMC1" "MCM5" "FEN1" "MCM7" "MCM10"
## [86] "RRM1" "MIR4435-2HG" "LGMN" "IL2RA" "KNTC1"
## [91] "F5" "ADTRP" "SELL" "KHDC1" "HIST1H3G"
## [96] "HIST1H3F" "HIST1H2BH" "HIST1H3D" "CHTF18" "HIST1H2BF"
## [101] "HIST1H2AL" "CKS1B" "HIST1H2AI" "HIST1H2AG" "HIST2H4B"
## [106] "HIST1H2BB" "HIST1H3C" "SBF2" "CENPS"
##
## $black
## [1] "GAPDH" "ACTB" "PFN1" "CFL1" "ACTG1"
## [6] "RPL28" "RPL18A" "RPL41" "RPS15" "RPL27A"
## [11] "RPL13A" "RPS28" "RPS19" "RPL11" "RPS12"
## [16] "RPS23" "RPS29" "RPS18" "RPS27" "RPL10"
## [21] "RPL18" "RPL37" "RPS16" "B2M" "RPLP1"
## [26] "RPS2" "RPS27A" "RPL37A" "RPS15A" "RPLP2"
## [31] "PTMA" "LTB" "JUNB" "SCD5" "SPON1"
## [36] "ANXA2" "DAD1" "AC022075.1" "NDUFA6" "FKBP1A"
## [41] "PKM" "BCAT1" "FABP5" "NUTF2" "LSM5"
## [46] "PRDX1" "ATP5F1E" "TMSB10" "RPS24"saveRDS(mods3, "~/gibbs/DOGMAMORPH/Ranalysis/modules/20230529ProliferatingModules.rds")
#in these cases, it doesnt make a lot of sense to go through and merge modules based on similarity. We're trying to preserve differences, so we may want to be able to preserve these separations even if things end up harder to analyze in the short term devtools::session_info()## Warning in system("timedatectl", intern = TRUE): running command 'timedatectl'
## had status 1## - Session info ---------------------------------------------------------------
## setting value
## version R version 4.2.0 (2022-04-22)
## os Red Hat Enterprise Linux 8.7 (Ootpa)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate C
## ctype C
## tz Etc/UTC
## date 2023-05-31
## pandoc 2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
##
## - Packages -------------------------------------------------------------------
## package * version date (UTC) lib source
## abind 1.4-5 2016-07-21 [2] CRAN (R 4.2.0)
## AnnotationDbi 1.60.2 2023-03-10 [1] Bioconductor
## backports 1.4.1 2021-12-13 [2] CRAN (R 4.2.0)
## base64enc 0.1-3 2015-07-28 [2] CRAN (R 4.2.0)
## Biobase 2.58.0 2022-11-01 [1] Bioconductor
## BiocGenerics 0.44.0 2022-11-01 [1] Bioconductor
## BiocParallel 1.32.6 2023-03-17 [1] Bioconductor
## Biostrings 2.66.0 2022-11-01 [1] Bioconductor
## bit 4.0.5 2022-11-15 [2] CRAN (R 4.2.0)
## bit64 4.0.5 2020-08-30 [2] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [2] CRAN (R 4.2.0)
## blob 1.2.4 2023-03-17 [1] CRAN (R 4.2.0)
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.2.0)
## cachem 1.0.8 2023-05-01 [1] CRAN (R 4.2.0)
## callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.0)
## checkmate 2.1.0 2022-04-21 [2] CRAN (R 4.2.0)
## cli 3.6.1 2023-03-23 [1] CRAN (R 4.2.0)
## cluster 2.1.4 2022-08-22 [2] CRAN (R 4.2.0)
## codetools 0.2-19 2023-02-01 [2] CRAN (R 4.2.0)
## colorspace 2.1-0 2023-01-23 [2] CRAN (R 4.2.0)
## cowplot * 1.1.1 2020-12-30 [2] CRAN (R 4.2.0)
## crayon 1.5.2 2022-09-29 [2] CRAN (R 4.2.0)
## data.table 1.14.8 2023-02-17 [2] CRAN (R 4.2.0)
## DBI 1.1.3 2022-06-18 [2] CRAN (R 4.2.0)
## deldir 1.0-6 2021-10-23 [2] CRAN (R 4.2.0)
## devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.0)
## digest 0.6.31 2022-12-11 [2] CRAN (R 4.2.0)
## doParallel * 1.0.17 2022-02-07 [1] CRAN (R 4.2.0)
## dplyr * 1.1.2 2023-04-20 [1] CRAN (R 4.2.0)
## dynamicTreeCut * 1.63-1 2016-03-11 [2] CRAN (R 4.2.0)
## ellipsis 0.3.2 2021-04-29 [2] CRAN (R 4.2.0)
## evaluate 0.20 2023-01-17 [2] CRAN (R 4.2.0)
## fansi 1.0.4 2023-01-22 [2] CRAN (R 4.2.0)
## fastcluster * 1.2.3 2021-05-24 [2] CRAN (R 4.2.0)
## fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.2.0)
## fastmatch 1.1-3 2021-07-23 [2] CRAN (R 4.2.0)
## fitdistrplus 1.1-8 2022-03-10 [2] CRAN (R 4.2.0)
## flashClust * 1.01-2 2012-08-21 [1] CRAN (R 4.2.0)
## foreach * 1.5.2 2022-02-02 [2] CRAN (R 4.2.0)
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## Formula 1.2-5 2023-02-24 [1] CRAN (R 4.2.0)
## fs 1.6.1 2023-02-06 [2] CRAN (R 4.2.0)
## future 1.32.0 2023-03-07 [1] CRAN (R 4.2.0)
## future.apply 1.10.0 2022-11-05 [1] CRAN (R 4.2.0)
## generics 0.1.3 2022-07-05 [2] CRAN (R 4.2.0)
## GenomeInfoDb 1.34.9 2023-02-02 [1] Bioconductor
## GenomeInfoDbData 1.2.9 2023-03-17 [1] Bioconductor
## GenomicRanges 1.50.2 2022-12-16 [1] Bioconductor
## ggplot2 * 3.4.2 2023-04-03 [1] CRAN (R 4.2.0)
## ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.2.0)
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## GO.db 3.16.0 2023-03-17 [1] Bioconductor
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## highr 0.10 2022-12-22 [1] CRAN (R 4.2.0)
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## htmlTable 2.4.1 2022-07-07 [1] CRAN (R 4.2.0)
## htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.2.0)
## htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.2.0)
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## httr 1.4.5 2023-02-24 [1] CRAN (R 4.2.0)
## ica 1.0-3 2022-07-08 [2] CRAN (R 4.2.0)
## igraph 1.4.2 2023-04-07 [1] CRAN (R 4.2.0)
## impute 1.72.3 2023-01-19 [1] Bioconductor
## IRanges 2.32.0 2022-11-01 [1] Bioconductor
## irlba 2.3.5.1 2022-10-03 [1] CRAN (R 4.2.0)
## iterators * 1.0.14 2022-02-05 [2] CRAN (R 4.2.0)
## jquerylib 0.1.4 2021-04-26 [2] CRAN (R 4.2.0)
## jsonlite 1.8.4 2022-12-06 [2] CRAN (R 4.2.0)
## KEGGREST 1.38.0 2022-11-01 [1] Bioconductor
## KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.0)
## knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
## later 1.3.0 2021-08-18 [2] CRAN (R 4.2.0)
## lattice 0.21-8 2023-04-05 [1] CRAN (R 4.2.0)
## lazyeval 0.2.2 2019-03-15 [2] CRAN (R 4.2.0)
## leiden 0.4.3 2022-09-10 [1] CRAN (R 4.2.0)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
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## lmtest 0.9-40 2022-03-21 [2] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [2] CRAN (R 4.2.0)
## MASS 7.3-59 2023-04-21 [1] CRAN (R 4.2.0)
## Matrix 1.5-4 2023-04-04 [1] CRAN (R 4.2.0)
## matrixStats 0.63.0 2022-11-18 [2] CRAN (R 4.2.0)
## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.2.0)
## mime 0.12 2021-09-28 [2] CRAN (R 4.2.0)
## miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.2.0)
## munsell 0.5.0 2018-06-12 [2] CRAN (R 4.2.0)
## nlme 3.1-162 2023-01-31 [1] CRAN (R 4.2.0)
## nnet 7.3-19 2023-05-03 [1] CRAN (R 4.2.0)
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## pbapply 1.7-0 2023-01-13 [1] CRAN (R 4.2.0)
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## pkgbuild 1.4.0 2022-11-27 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.2.0)
## pkgload 1.3.2 2022-11-16 [1] CRAN (R 4.2.0)
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## plyr 1.8.8 2022-11-11 [1] CRAN (R 4.2.0)
## png 0.1-8 2022-11-29 [1] CRAN (R 4.2.0)
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## purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
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## ROCR 1.0-11 2020-05-02 [2] CRAN (R 4.2.0)
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## Rsamtools 2.14.0 2022-11-01 [1] Bioconductor
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## sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.2.0)
## Seurat * 4.3.0 2022-11-18 [1] CRAN (R 4.2.0)
## SeuratObject * 4.1.3 2022-11-07 [1] CRAN (R 4.2.0)
## shiny 1.7.4 2022-12-15 [1] CRAN (R 4.2.0)
## Signac * 1.9.0 2022-12-08 [1] CRAN (R 4.2.0)
## sp 1.6-0 2023-01-19 [1] CRAN (R 4.2.0)
## spatstat.data 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.explore 3.1-0 2023-03-14 [1] CRAN (R 4.2.0)
## spatstat.geom 3.1-0 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.random 3.1-4 2023-03-13 [1] CRAN (R 4.2.0)
## spatstat.sparse 3.0-1 2023-03-12 [1] CRAN (R 4.2.0)
## spatstat.utils 3.0-2 2023-03-11 [1] CRAN (R 4.2.0)
## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.0)
## stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.0)
## survival 3.5-5 2023-03-12 [1] CRAN (R 4.2.0)
## tensor 1.5 2012-05-05 [2] CRAN (R 4.2.0)
## tibble 3.2.1 2023-03-20 [1] CRAN (R 4.2.0)
## tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.2.0)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
## uwot 0.1.14 2022-08-22 [1] CRAN (R 4.2.0)
## vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.2.0)
## viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.2.0)
## WGCNA * 1.72-1 2023-01-18 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [2] CRAN (R 4.2.0)
## xfun 0.39 2023-04-20 [1] CRAN (R 4.2.0)
## xtable 1.8-4 2019-04-21 [2] CRAN (R 4.2.0)
## XVector 0.38.0 2022-11-01 [1] Bioconductor
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
## zip 2.3.0 2023-04-17 [1] CRAN (R 4.2.0)
## zlibbioc 1.44.0 2022-11-01 [1] Bioconductor
## zoo 1.8-12 2023-04-13 [1] CRAN (R 4.2.0)
##
## [1] /gpfs/gibbs/project/ya-chi_ho/jac369/R/4.2
## [2] /vast/palmer/apps/avx2/software/R/4.2.0-foss-2020b/lib64/R/library
##
## ------------------------------------------------------------------------------